Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hdac3

Cell type

Cell type Class
Lung
Cell type
Lung tumors
NA
NA

Attributes by original data submitter

Sample

source_name
Primary Kras-mutant, Lkb1-/- NSCLC tumor
tissue
primary NSCLC tumor
genotype
Kras-mutant, Lkb1-/-
treatment
none
guide rna
none
chip antibody
HDAC3
antibody source
ab7030

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, cells were collected and cross-linked in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, nuclei were isolated and then sheared in a Covaris E229 sonicator for 8 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Hdac3 or H3K27ac then bound to Protein A Dynabeads (Invitrogen). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
41390853
Reads aligned (%)
85.5
Duplicates removed (%)
8.6
Number of peaks
521 (qval < 1E-05)

mm9

Number of total reads
41390853
Reads aligned (%)
85.5
Duplicates removed (%)
8.7
Number of peaks
496 (qval < 1E-05)

Base call quality data from DBCLS SRA